ChIP-seq and FAIRE-seq/ Find motifs with GADEM and match to JASPAR


Given a set of genomic regions, this tool discovers sequence motifs and matches them against the JASPAR database of known transcription factor binding sites. For each motif, 10 best matches to JASPAR are reported.



For a thorough description of the technical details please consult the original publications cited in the References section below. Briefly, the analysis proceeds through the following steps:


The analysis output consists of the following:


This tool uses the following Bioconductor packages:

For more details refer to these publications:

S. Mahony, P.V. Benos "STAMP: a web tool for exploring DNA-binding motif similarities." Nucl Acids Res, (2007) 35:W253-258

S Mahony, PE Auron, PV Benos, "DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies", PLoS Computational Biology (2007) 3(3):e61

L. Leiping. GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery. J Comput Biology, (2009) Feb;16(2):317-29.